[tomsem]

I would (and have) crop the top/bottom margins before putting it on Kindle. It does help a little bit. The experience can be further improved by adding page labels (corresponding to what the book has), bookmarks, and any navigation links you might want. Paperwhite supports all of those things.

If you want on device manual cropping, Sony Readers (or at least T series) do that, you can probably pick up a used one for well under $100.

I will not be one to tell you to use a tablet, as if you had not considered that. The PDF support of Paperwhite is useful enough, better than that of many other ereaders, and it's an option I wouldn't want to be without.